Nick Fury tells Maria Hill "I need you to make sure that phase two prototypes are shipped out". Continued: "Clear out the deck below, every piece of phase two in a truck and gone."

I took it as Marvel's Phase 2 with more possible avengers.

SPOILERS BELOW!!! I HAVEN'T MASTERED THE TAGS IF YOU HAVEN'T SEEN THE FILM DON'T READ.

I thought the same but it's explain later that phase 2 is actually using the cube and Hydra tech to make WMDs. There is also the reference to Jane Foster and why she isn't around(SHIELD MOVED HER TO A SECLUDED BASE IN TROMSO, WHICH MUST BE HARDER TO GET TO THAT STUTTGART) during the conversation between Thor and Coulson, I suppose even the gun that Coulson uses is an Easter Egg of sorts as it seeems to come from destroyer tech.